Ion channels are important biological devices used to control the passage of ions across membranes, selecting some and rejecting others, and to transmit information in response to particular stimuli: electrical (Na+ and K+ pores which propagate neuronal signals along axons), chemical (synapses), visual (retinal photoreceptors) and mechanical (mechanoreceptors). Our aim is to understand the microscopic basis of ion transport through channels in terms of molecular dynamics, the motion of the atoms, and to use this knowledge to design new channels with different ion selective properties. Our method is to use molecular dynamics, to compute from classical mechanics and atomic trajectories on the relevant potential surface in order to follow for a particularly simple and well studied ion channel, the antibiotic gramicidin-A, the dynamic details of peptide distortion, ion motion and solvation, the participation of water molecules inside the channel. Then we will alter the chemical structure of the gramicidin-A and compute the resulting changes in ion conductivity and selectivity. Thus we propose to use the tool of molecular dynamics to study the atomic motions which give rise to an actual biological effect. To our knowledge, this would be the first time that structure, dynamics and biological action have been successfully computed for a molecule of the complexity of a polypeptide, and the first time that changes in biological activity with changes in structure would be predicted and analyzed using molecular dynamics. Our long-term objectives are to develop a deeper understanding of how ion transport through channels takes place, to learn how to control ion transport properties by chemical alteration of the channel, to develop molecular dynamics for further application to other important biological systems, and to begin to extend our understanding of biomolecular processes from structure-function relationships to a more general understanding in terms of structure, dynamics and function.